LXL04_011604 | RubberDandelionOmics

Gene overview

LXL04_011604

Reference: OH-1004 Chr: Chr02 Coordinates: 168044832-168046443 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1260 bp · LXL04_011604|LXL04_011604|OH1004|cDNA

ATGGGAGGCACCGATCAAGTTCGCGGCACCAGACGTTCGCCGGCAGCAACCAACGGCGGCGTTGTAATCACCAGAAACCTAGACTCAGATGCCGTCATCAATCTAGACCATGGGGATCCGACGATGTACGAGTCTTTTTGGAGAAAAATGGGGGACAAGTGTACGGTTGTGTTTAAAGGGCATGAATCTTTAAGTTACTTTTCAAACGTCAAGAACCCTTGTTGGTTTCTTGAACCGAAACTTGAAGACTCGATCAAGAG...

CDS

Download CDS FASTA

1260 bp · LXL04_011604|LXL04_011604|OH1004|CDS

ATGGGAGGCACCGATCAAGTTCGCGGCACCAGACGTTCGCCGGCAGCAACCAACGGCGGCGTTGTAATCACCAGAAACCTAGACTCAGATGCCGTCATCAATCTAGACCATGGGGATCCGACGATGTACGAGTCTTTTTGGAGAAAAATGGGGGACAAGTGTACGGTTGTGTTTAAAGGGCATGAATCTTTAAGTTACTTTTCAAACGTCAAGAACCCTTGTTGGTTTCTTGAACCGAAACTTGAAGACTCGATCAAGAG...

Protein

Download Protein FASTA

419 aa · LXL04_011604|LXL04_011604|OH1004|PROTEIN

MGGTDQVRGTRRSPAATNGGVVITRNLDSDAVINLDHGDPTMYESFWRKMGDKCTVVFKGHESLSYFSNVKNPCWFLEPKLEDSIKSLHGAVGNAVTDGYSIVVGTGSSQLLQAVLYAVSRDQTTQMNVVSPAPYYSSYPEIIDLVKSGLYKWAGDAYVFDKDEPYIELVTSPNNPNGVIRGAVVNRDDGILIHDLAYYWPQYTPITSSLSFDIMLFTASKCTGHAGSRIGWALVKDKEVAKRMTKYIEVNTIGVSKESQ...

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

ID Mapping

Input ID	`LXL04_011604`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_011604

Location Chr02:168044832-168046443 (+)

Description Similar to TAA1: L-tryptophan--pyruvate aminotransferase 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g70560`	L-tryptophan aminotransferase involved in auxin (IAA) biosynthesis.	Rapid synthesis of auxin via a new tryptophan-dependent pathway is required for shade avoidance in plants.2008 · DOI: 10.1016/j.cell.2008.01.049 TAA1-mediated auxin biosynthesis is essential for hormone crosstalk and plant development.2008 · DOI: 10.1016/j.cell.2008.01.047
`At4g24670`	Involved in auxin production.	No verified direct reference in this release
`At1g23320`	Probably involved in auxin production.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os05g0169300`	Probable tryptophan aminotransferase that may be involved in the regulation of auxin production in developing rice grains.	A large increase in IAA during development of rice grains correlates with the expression of tryptophan aminotransferase OsTAR1 and a grain-specific YUCCA.2012 · DOI: 10.1111/j.1399-3054.2012.01649.x
`Os01g0169800`	Probable tryptophan aminotransferase involved in auxin (IAA) biosynthesis.	The YUCCA-Auxin-WOX11 Module Controls Crown Root Development in Rice.2018 · DOI: 10.3389/fpls.2018.00523

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_011604 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006520 amino acid metabolic process Biological Process

GO:0009641 shade avoidance Biological Process

GO:0009684 indoleacetic acid biosynthetic process Biological Process

GO:0009723 response to ethylene Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0009851 auxin biosynthetic process Biological Process

GO:0009908 flower development Biological Process

GO:0009926 auxin polar transport Biological Process

GO:0009958 positive gravitropism Biological Process

GO:0010078 maintenance of root meristem identity Biological Process

GO:0010087 phloem or xylem histogenesis Biological Process

GO:0010588 cotyledon vascular tissue pattern formation Biological Process

KEGG gene cross-reference

ath:AT1G23320

ath:AT1G70560

ath:AT4G24670

dosa:Os01g0169800

dosa:Os05g0169300

osa:4337930

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene

Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Cytoplasm0.485

Rank 1 · LXL04_011604 · OH-1004

Nucleus0.300

Rank 2 · LXL04_011604 · OH-1004

Endoplasmic reticulum0.101

Rank 3 · LXL04_011604 · OH-1004

Cell membrane0.078

Rank 4 · LXL04_011604 · OH-1004

Lysosome / Vacuole0.057

Rank 5 · LXL04_011604 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF04864.20Alliinase_C33-390 aa

PF00155.28Aminotran_1_278-387 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_011604	`PF04864.20`	Alliinase_C	33	390	2.9e-143	477.9
LXL04_011604	`PF00155.28`	Aminotran_1_2	78	387	1.7e-11	44.7

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9S7N2`	Arabidopsis thaliana	L-tryptophan--pyruvate aminotransferase 1	57.641%	Swiss-Prot	strong database homology
`Q94A02`	Arabidopsis thaliana	Tryptophan aminotransferase-related protein 2	56.486%	Swiss-Prot	strong database homology
`Q9LR29`	Arabidopsis thaliana	Tryptophan aminotransferase-related protein 1	53.533%	Swiss-Prot	strong database homology
`Q0DKE8`	Oryza sativa subsp. japonica	Tryptophan aminotransferase-related protein 1	54.472%	Swiss-Prot	strong database homology
`Q5VQG8`	Oryza sativa subsp. japonica	Tryptophan aminotransferase-related protein 2	51.515%	Swiss-Prot	strong database homology

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